Biochemistry of Metabolism

Review:
Basic Concepts of Protein Structure

Note: It is assumed that students will be
already familiar with basic concepts of protein and nucleic acid structure, as
well as enzyme kinetics and mechanisms, before using the Biochemistry of
Metabolism educational web. A review of some elementary
concepts relating to protein structure is provided here. For a more complete discussion see, e.g., Biochemistry by D. Voet
& J. G. Voet, 3rd Ed, chapters 4, 7 & 8.

Each amino acid has the same fundamental structure, differing only in
the side-chain, designated the R-group. The
carbon atom to which the amino group, carboxyl group, and side chain (R-group)
are attached is the
alpha carbon (Ca).

Structures of amino acids, with their R-groups in blue, are shown below
with their three-letter and one-letter abbreviated names.
Glycine has just a hydrogen atom in place of an R-group. At physiological pH,
some amino acid R-groups are charged, because of dissociation or association of
a proton by, e.g., a carboxyl or amino group. Note that histidine is shown
charged, but its pK is close to the physiological range. Some
side-chain groups that are uncharged at the near-neutral pH of the cytosol or extracellular
space, may dissociate or gain a proton in the microenvironment of an enzyme
active site.

Peptide bonds link amino acid
residues within proteins. The sequence of covalently linked amino acids is
known as the primary structure of a
protein.

The reaction by which two amino acids are joined in a peptide bond, with elimination of H2O, is
represented at right. For detail on the mechanism of peptide bond formation, see the section
on protein synthesis.

A protein is a polypeptide, a linear polymer of many amino acids, linked by peptide bonds.

The peptide linkages, along with the a-carbon
atoms to which R-groups are attached, form the protein backbone,
with sequence NCCNCCNCCNCC...

Protein Secondary Structure.Segments of polypeptides often fold locally into stable structures that
include a-helices and b-pleated
sheets.

a-Helix.
In an a-helix
(alpha helix), the polypeptide backbone
follows a helical
path. There are 3.6 amino acid residues per turn of the helix. Some protein
domains
assume other helical structures, but the a-helix
is most common.

An a-helix is stabilized by hydrogen bonds between backbone amino
and carbonyl groups and those in the next turn of the helix, represented as N-H····O=C.
The hydrogen and oxygen atoms are attracted to one another because the H
atom carries a partial positive charge and the O atom carries a partial
negative charge, due to unequal sharing of electrons in N-H and O=C bonds.
Diagram p. 224 of
Voet & Voet text.

In an a-helix, the amino acid
R-groups protrude out from the helically
coiled polypeptide backbone. The surface of
an a-helix largely consists of the R-groups of
amino acid residues.

At right, an a-helix is shown end-on and from the side. In this image, H atoms are not visible. Colors: CNOR-group

Some amino acids have a greater tendency to be found
within an a-helix. The amino acid proline tends to
interrupt an a-helix. Its fused ring,
which includes the a-carbon and the peptide-forming
amino N, prevents the polypeptide backbone from assuming a conformation compatible with
an a-helix in the vicinity of a proline.

Explore below the structure of an
a-helix, using MDL's software plug-in Chime. Note
that with this data file hydrogen atoms will not be visible. For a
tutorial on the Chime software, see
Chime: How to use it , a website maintained by Eric Martz.

With the cursor on the image below, click down on the right mouse button to choose from menus.

With Chime, usually one selects something, and then alters its
display, color, etc.

Use the left mouse button to
drag the image to view the
a-helix from different perspectives.

Using the right mouse button, choose displaybackbone.
Drag to view
the
spiraling backbone from the side as well as down its axis.

Now choose displayball & stick with
colorCPK (a color convention in which
C is grey, O is red, N is blue, etc.)
To distinguish the R-groups, select
protein-sidechain, and then display as
sticks.

Identify atoms of the protein
backbone with sequence NCCNCCNCCNCC...
Hold down the shift key
and left-drag to zoom in for a closer look.

Question: Structures of individual
amino acids are given above. Based on the R-group structures, identify each amino acid residue and
specify the sequence of amino acids in this peptide.

Now selectprotein - sidechain; then select - change color to and
pick a color.
This will give the R-groups a color
distinct from the CPK-colored backbone atoms.

Questions:
What part of the polypeptide is mainly exposed to the
surrounding medium.
Is an a-helix a hollow structure?

CONS

Beta pleated sheets. Another
common secondary structure is the b
sheet (beta sheet). In a b sheet, strands
of protein lie adjacent to one another, interacting laterally via H bonds
between backbone carbonyl oxygen and amino H atoms. The strands may be parallel (N-termini of both strands at the
same end) or antiparallel. See diagrams p.
228-229 of Voet & Voet.

Because of the tetrahedral nature of carbon bonds, a b-sheet
is puckered, leading to the designation pleated
sheet.

R groups of amino acids in a b-strand
alternately point to one side or the other of a b-strand.
Hence every other amino acid is exposed on one side or the other of a
b-sheet.

Explore at right two strands of a
b-sheet (Data file derived from
PDB 1ICM). Recommended displays:

Display as cartoon. Question: Are the two
b-strands parallel or antiparallel?

Now change the display to ball & stick,
with color CPK.
Then select protein-sidechain, and
select-change color to. Specify a color
not already visible, such as green.

View the 2-stranded
b-sheet from the side. Note the "pleated" appearance of
each b-strand.Note how the protein side-chains
(R-groups) alternate in extending above and below the b-sheet.Note how, within the plane of the sheet, backbone carbonyl oxygen atoms
point toward backbone amino N atoms of the adjacent strand. (H atoms
involved in interchain H-bonds are not visible in this structure, which is
based on X-ray crystallographic analysis.)

These two b-strands are actually part of a
larger protein that you will explore
below.

CONS

A common structural motif, the b-barrel,
is equivalent to a b-sheet that is rolled up to
form a cylinder. An example of a protein that consists mainly of a b-barrel is the bacterial channel porin.

In some cases, a b-barrel may be partly
flattened, to form what is called a b-clam
structure (see below).

Other common folding motifs involve combinations of a-helices and
b-strands. One example is the a,b-barrel,
explored elsewhere in an exercise on Triose
Phosphate Isomerase (TIM).

Display as
cartoon, and color structure. Different colors distinguish the
b-strands, a-helices and
sharp turns called hairpin loops.

Question: Would you describe the predominant
structure as a b-sheet, b-barrel, or b-clam?

To view the fatty acid, select
hetero-ligand and display as spacefill
with color CPK. Now select protein-protein
and display as spacefill with color chain.
Is the fatty acid well enclosed by its binding protein?

Tertiary protein structure
refers to the complete three dimensional folding of a protein. Stabilization of
a protein's tertiary structure may involve interactions between amino acids
located far apart along the primary sequence. These may include:

disulfide bonds, covalent linkages
that may
form as the thiol groups of two cysteine residues are oxidized to a disulfide:
2R-SH®R-S-S-R.

Interactions with the aqueous solvent, known as the
hydrophobic effect results in residues with non-polar side-chains
typically being buried in the interior of a protein. Conversely, polar
amino acid side-chains tend to on the surface of a protein where they are exposed to
the aqueous milieu. There are, however, many exceptions in which polar residues
are buried or non-polar residues exposed on the surface of a protein. Such
atypical locations might be stabilized, e.g., by interaction of amino acid side-chains with enzyme prosthetic
groups or other ligands, by interactions between amino acid side-chains, or by
association of proteins with lipid membranes,
etc.

Many proteins have a modular design with
multiple distinct domains resulting from gene fusion events during evolution. A
domain with a particular structure and function may be part of the structure of
several otherwise distinct proteins. For example, an enzyme's primary structure
may include a segment that folds to produce an active site with particular
catalytic activity, plus other segments that may mediate regulation of the
enzyme or binding of the enzyme to a membrane.

Quaternary protein structure
refers to the regular association of two or more polypeptide chains to form a
complex. A multi-subunit protein may be composed of two or more identical
polypeptides, or it may include different polypeptides. Quaternary structure
tends to be stabilized mainly by weak interactions between residues exposed on surfaces
polypeptides within a complex.

A multimeric complex may be important to enzyme activity, e.g., in cases
in which an active site is formed by residues from more than one polypeptide
subunit, or when adjacent active sites may be involved sequentially in
catalysis of a complex reaction. Regulation of functional activity may
involve cooperative interactions among protein subunits in a complex.
Examples of these are included throughout this web.